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Author Details

Alan P Boyle
University of Michigan ann arbor
2008
50
26
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36712073LRphase: an efficient method for assigning haplotype identity to long reads.bioRxiv2023
37156622Multiplexed long-read plasmid validation and analysis using OnRamp.Genome Res2023
36712073LRphase: an efficient method for assigning haplotype identity to long reads.bioRxiv2023
37460896Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1.Nat Struct Mol Biol2023
37305558Challenges in screening for <i>de novo</i> noncoding variants contributing to genetically complex phenotypes.HGG Adv2023
37173523Annotating and prioritizing human non-coding variants with RegulomeDB v.2.Nat Genet2023
37460896Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1.Nat Struct Mol Biol2023
37156622Multiplexed long-read plasmid validation and analysis using OnRamp.Genome Res2023
37173523Annotating and prioritizing human non-coding variants with RegulomeDB v.2.Nat Genet2023
37305558Challenges in screening for <i>de novo</i> noncoding variants contributing to genetically complex phenotypes.HGG Adv2023
34648033Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.Nucleic Acids Res2022
35927613SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.BMC Bioinformatics2022
34648033Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.Nucleic Acids Res2022
35927613SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.BMC Bioinformatics2022
34117247Cas9 targeted enrichment of mobile elements using nanopore sequencing.Nat Commun2021
34117247Cas9 targeted enrichment of mobile elements using nanopore sequencing.Nat Commun2021
34220959The Inducible <i>lac</i> Operator-Repressor System Is Functional in Zebrafish Cells.Front Genet2021
33655209F-Seq2: improving the feature density based peak caller with dynamic statistics.NAR Genom Bioinform2021
34706748SquiggleNet: real-time, direct classification of nanopore signals.Genome Biol2021
33655209F-Seq2: improving the feature density based peak caller with dynamic statistics.NAR Genom Bioinform2021
34706748SquiggleNet: real-time, direct classification of nanopore signals.Genome Biol2021
34220959The Inducible <i>lac</i> Operator-Repressor System Is Functional in Zebrafish Cells.Front Genet2021
32286261Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.Nat Commun2020
32051932Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.NAR Genom Bioinform2020
32286261Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.Nat Commun2020
33199612Broad noncoding transcription suggests genome surveillance by RNA polymerase V.Proc Natl Acad Sci U S A2020
32962625MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.BMC Bioinformatics2020
32660981TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.Genome Res2020
32051932Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.NAR Genom Bioinform2020
33199612Broad noncoding transcription suggests genome surveillance by RNA polymerase V.Proc Natl Acad Sci U S A2020
32660981TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.Genome Res2020
32962625MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.BMC Bioinformatics2020
30593493Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.Genetics2019
32500114CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.J Open Source Softw2019
30593493Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression.Genetics2019
31106481Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.Hum Mutat2019
31249361The ENCODE Blacklist: Identification of Problematic Regions of the Genome.Sci Rep2019
32500114CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.J Open Source Softw2019
31249361The ENCODE Blacklist: Identification of Problematic Regions of the Genome.Sci Rep2019
31106481Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.Hum Mutat2019
29290336Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.Am J Hum Genet2018
29290336Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.Am J Hum Genet2018
29361190Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.Nucleic Acids Res2018
29361190Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.Nucleic Acids Res2018
27939749Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.Trends Genet2017
28541271Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve.Nat Commun2017
29187152A proximity-based graph clustering method for the identification and application of transcription factor clusters.BMC Bioinformatics2017
27939749Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.Trends Genet2017
29187152A proximity-based graph clustering method for the identification and application of transcription factor clusters.BMC Bioinformatics2017
28541271Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve.Nat Commun2017
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Collaborators

Michael Snyder
Stanford University
Co-authored papers 13
Anshul Kundaje
Stanford University.
Co-authored papers 9
Terrence S Furey
University of North Carolina at Chapel Hill
Co-authored papers 9
Gregory E Crawford
Center for Genomic & Computational Biology, Duke University
Co-authored papers 7
Trupti Kawli
Co-authored papers 6
Yong Cheng
Co-authored papers 6
Lingyun Song
Center for Genomic & Computational Biology, Duke University
Co-authored papers 5
Philip Cayting
Co-authored papers 4
Ghia Euskirchen
Co-authored papers 4
Bum-Kyu Lee
Cancer Research Center, University at Albany, State University of New York
Co-authored papers 3
Ewan Birney
European Bioinformatics Institute
Co-authored papers 3
Vishwanath R Iyer
Indian Institute of Technology Bombay
Co-authored papers 3
Damian Keefe
University of Adelaide
Co-authored papers 3
Serafim Batzoglou
Co-authored papers 3
Manoj Hariharan
Co-authored papers 3
Manolis Kellis
Massachusetts Institute of Technology
Co-authored papers 3
Mark Gerstein
Yale University
Co-authored papers 3
Douglas H Phanstiel
University of North Carolina at Chapel Hill
Co-authored papers 2
Dorrelyn Patacsil
Co-authored papers 2
Jingjing Li
Co-authored papers 2
Jinmin Lian
Co-authored papers 2
Joel Rozowsky
Co-authored papers 2
Weichen Zhou
Chengdu First People's Hospital
Co-authored papers 2
Ryan M McDaniell
The Children's Hospital of Philadelphia
Co-authored papers 2
Ryan E Mills
University of Michigan Medical School ann arbor
Co-authored papers 2
Zhiping Weng
University of Massachusetts Medical School
Co-authored papers 2
Laura J Scott
Co-authored papers 2
Stephen C J Parker
University of Michigan ann arbor
Co-authored papers 2
Ross C Hardison
Co-authored papers 2
Sherman M Weissman
Co-authored papers 2
Release 1.2